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Aliases for NPRL3 Gene

Aliases for NPRL3 Gene

  • NPR3 Like, GATOR1 Complex Subunit 2 3 5
  • Alpha-Globin Regulatory Element-Containing Gene Protein 3 4
  • Conserved Gene Telomeric To Alpha Globin Cluster 2 3
  • -14 Gene Protein 3 4
  • C16orf35 3 4
  • CGTHBA 3 4
  • MARE 3 4
  • Nitrogen Permease Regulator-Like 3 (S. Cerevisiae) 2
  • Nitrogen Permease Regulator 3-Like Protein 3
  • Chromosome 16 Open Reading Frame 35 2
  • NPR3-Like, GATOR1 Complex Subunit 2
  • Protein CGTHBA 4
  • FFEVF3 3
  • HS-40 3
  • RMD11 3
  • NPR3 3

External Ids for NPRL3 Gene

Previous HGNC Symbols for NPRL3 Gene

  • C16orf35

Previous GeneCards Identifiers for NPRL3 Gene

  • GC16M000134
  • GC16M000054

Summaries for NPRL3 Gene

Entrez Gene Summary for NPRL3 Gene

  • The function of the encoded protein is not known. [provided by RefSeq, Aug 2011]

GeneCards Summary for NPRL3 Gene

NPRL3 (NPR3 Like, GATOR1 Complex Subunit) is a Protein Coding gene. Diseases associated with NPRL3 include Epilepsy, Familial Focal, With Variable Foci and Secondary Hypertrophic Osteoarthropathy. Among its related pathways are mTOR signaling pathway (KEGG). GO annotations related to this gene include GTPase activator activity.

UniProtKB/Swiss-Prot for NPRL3 Gene

  • As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the TORC1 pathway. The GATOR1 complex strongly increases GTP hydrolysis by RRAGA and RRAGB within RRAGC-containing heterodimers, thereby deactivating RRAGs, releasing mTORC1 from lysosomal surface and inhibiting mTORC1 signaling. The GATOR1 complex is negatively regulated by GATOR2 the other GATOR subcomplex in this amino acid-sensing branch of the TORC1 pathway.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NPRL3 Gene

Genomics for NPRL3 Gene

Regulatory Elements for NPRL3 Gene

Enhancers for NPRL3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16G000137 1.3 ENCODE dbSUPER 36.8 +0.7 659 2.2 HDGF PKNOX1 CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 NPRL3 RHOT2 CAPN15 WASH4P JMJD8 GC16P000151
GH16G000066 1.8 FANTOM5 ENCODE dbSUPER 22.4 +65.4 65359 13.6 HDGF PKNOX1 ARNT MLX CREB3L1 AGO1 ZFP64 ARID4B SIN3A DMAP1 NPRL3 RHOT2 CAPN15 WASH4P MPG JMJD8 ENSG00000228779 HBZ HBM SNRNP25
GH16G000065 1.5 Ensembl ENCODE dbSUPER 21.8 +72.9 72918 0.5 HDGF ATF1 ARID4B SIN3A ZNF2 ZNF48 SLC30A9 ZNF143 ZNF207 DEK NPRL3 ENSG00000228779 GC16P000130 POLR3K
GH16G000101 0.9 ENCODE dbSUPER 31.8 +36.3 36343 2.0 ESRRA ZNF362 ZBTB11 NR4A1 CEBPB MAX ZBTB7A NR2F2 ZNF592 POLR2A NPRL3 ENSG00000228779 HBZ HBM SNRNP25 GC16P000124 GC16P000121
GH16G000113 1.3 ENCODE dbSUPER 19.5 +25.2 25219 2.4 HNRNPUL1 HDGF PKNOX1 CREB3L1 MLX ARNT ARID4B SLC30A9 ZNF766 FOS NPRL3 HBZ HBM WFIKKN1 GC16P000124 ENSG00000228779
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NPRL3 on UCSC Golden Path with GeneCards custom track

Promoters for NPRL3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000082133 360 1801 HDGF PKNOX1 CREB3L1 ARID4B DMAP1 ZNF2 ZNF143 ZNF207 KLF13 SP3

Genomic Location for NPRL3 Gene

Chromosome:
16
Start:
84,271 bp from pter
End:
138,860 bp from pter
Size:
54,590 bases
Orientation:
Minus strand

Genomic View for NPRL3 Gene

Genes around NPRL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NPRL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NPRL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NPRL3 Gene

Proteins for NPRL3 Gene

  • Protein details for NPRL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q12980-NPRL3_HUMAN
    Recommended name:
    Nitrogen permease regulator 3-like protein
    Protein Accession:
    Q12980
    Secondary Accessions:
    • D3DU40
    • Q1W6H0
    • Q4TT56
    • Q92469

    Protein attributes for NPRL3 Gene

    Size:
    569 amino acids
    Molecular mass:
    63605 Da
    Quaternary structure:
    • Forms a heterodimer with NPRL2. Within the GATOR complex, component of the GATOR1 subcomplex, made of DEPDC5, NPRL2 and NPRL3. GATOR1 mediates the strong interaction of the GATOR complex with RRAGA/RRAGC and RRAGB/RRAGC heterodimers.

neXtProt entry for NPRL3 Gene

Post-translational modifications for NPRL3 Gene

  • Ubiquitination at posLast=253253 and posLast=546546
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NPRL3 Gene

Domains & Families for NPRL3 Gene

Gene Families for NPRL3 Gene

Protein Domains for NPRL3 Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q12980

UniProtKB/Swiss-Prot:

NPRL3_HUMAN :
  • Belongs to the NPR3 family.
Family:
  • Belongs to the NPR3 family.
genes like me logo Genes that share domains with NPRL3: view

Function for NPRL3 Gene

Molecular function for NPRL3 Gene

UniProtKB/Swiss-Prot Function:
As a component of the GATOR1 complex functions as an inhibitor of the amino acid-sensing branch of the TORC1 pathway. The GATOR1 complex strongly increases GTP hydrolysis by RRAGA and RRAGB within RRAGC-containing heterodimers, thereby deactivating RRAGs, releasing mTORC1 from lysosomal surface and inhibiting mTORC1 signaling. The GATOR1 complex is negatively regulated by GATOR2 the other GATOR subcomplex in this amino acid-sensing branch of the TORC1 pathway.

Gene Ontology (GO) - Molecular Function for NPRL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005096 contributes_to GTPase activator activity IEA,IDA 23723238
genes like me logo Genes that share ontologies with NPRL3: view
genes like me logo Genes that share phenotypes with NPRL3: view

Animal Models for NPRL3 Gene

MGI Knock Outs for NPRL3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for NPRL3 Gene

Localization for NPRL3 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for NPRL3 gene
Compartment Confidence
lysosome 5
cytosol 3
mitochondrion 2
extracellular 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for NPRL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005765 lysosomal membrane IDA 28199306
GO:0005773 vacuole IBA --
GO:1990130 Iml1 complex IDA 23723238
genes like me logo Genes that share ontologies with NPRL3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for NPRL3 Gene

Pathways & Interactions for NPRL3 Gene

SuperPathways for NPRL3 Gene

SuperPathway Contained pathways
1 mTOR signaling pathway (KEGG)
genes like me logo Genes that share pathways with NPRL3: view

Pathways by source for NPRL3 Gene

1 KEGG pathway for NPRL3 Gene

Gene Ontology (GO) - Biological Process for NPRL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003281 ventricular septum development IEA --
GO:0008150 biological_process ND --
GO:0032007 negative regulation of TOR signaling IMP 23723238
GO:0034198 cellular response to amino acid starvation IMP 23723238
GO:0035909 aorta morphogenesis IEA --
genes like me logo Genes that share ontologies with NPRL3: view

No data available for SIGNOR curated interactions for NPRL3 Gene

Drugs & Compounds for NPRL3 Gene

No Compound Related Data Available

Transcripts for NPRL3 Gene

Unigene Clusters for NPRL3 Gene

Nitrogen permease regulator-like 3 (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NPRL3 Gene

No ASD Table

Relevant External Links for NPRL3 Gene

GeneLoc Exon Structure for
NPRL3
ECgene alternative splicing isoforms for
NPRL3

Expression for NPRL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NPRL3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for NPRL3 Gene

This gene is overexpressed in Whole Blood (x7.2).

Protein differential expression in normal tissues from HIPED for NPRL3 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (68.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NPRL3 Gene



NURSA nuclear receptor signaling pathways regulating expression of NPRL3 Gene:

NPRL3

SOURCE GeneReport for Unigene cluster for NPRL3 Gene:

Hs.19699

mRNA Expression by UniProt/SwissProt for NPRL3 Gene:

Q12980-NPRL3_HUMAN
Tissue specificity: Widely expressed. Expressed in the frontal lobe cortex as well as in the temporal, parietal, and occipital lobes (PubMed:27173016, PubMed:26505888).

Evidence on tissue expression from TISSUES for NPRL3 Gene

  • Liver(4.1)
  • Nervous system(3.3)
  • Lung(2.5)
  • Blood(2.4)
  • Eye(2.1)
genes like me logo Genes that share expression patterns with NPRL3: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NPRL3 Gene

Orthologs for NPRL3 Gene

This gene was present in the common ancestor of animals.

Orthologs for NPRL3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NPRL3 34 35
  • 99.51 (n)
dog
(Canis familiaris)
Mammalia NPRL3 34 35
  • 90.93 (n)
cow
(Bos Taurus)
Mammalia NPRL3 34 35
  • 89.93 (n)
oppossum
(Monodelphis domestica)
Mammalia NPRL3 35
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nprl3 34
  • 88.89 (n)
mouse
(Mus musculus)
Mammalia Nprl3 34 16 35
  • 88.83 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia NPRL3 35
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves CGTHBA 35
  • 86 (a)
OneToMany
NPRL3 34
  • 78.64 (n)
-- 35
  • 74 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia NPRL3 35
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nprl3 34
  • 72.12 (n)
Str.18308 34
African clawed frog
(Xenopus laevis)
Amphibia MGC68624 34
zebrafish
(Danio rerio)
Actinopterygii nprl3 34 35
  • 73.96 (n)
wufb68d06 34
fruit fly
(Drosophila melanogaster)
Insecta CG8783 34 35
  • 51.08 (n)
worm
(Caenorhabditis elegans)
Secernentea nprl-3 34 35
  • 39.66 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToOne
Species where no ortholog for NPRL3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NPRL3 Gene

ENSEMBL:
Gene Tree for NPRL3 (if available)
TreeFam:
Gene Tree for NPRL3 (if available)

Paralogs for NPRL3 Gene

(1) SIMAP similar genes for NPRL3 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with NPRL3: view

No data available for Paralogs for NPRL3 Gene

Variants for NPRL3 Gene

Sequence variations from dbSNP and Humsavar for NPRL3 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs200041907 Epilepsy, familial focal, with variable foci 3 (FFEVF3) [MIM:617118] 100,394(+) CCGTT(C/T)GATGG reference, missense
rs367729589 Epilepsy, familial focal, with variable foci 3 (FFEVF3) [MIM:617118] 119,169(+) CAAAT(C/T)GCACA intron-variant, reference, missense
rs886037958 Pathogenic 98,233(-) CTGCT(-/T)CCCCT reference, frameshift-variant
rs886037959 Pathogenic 88,891(-) CCCCC(ACAG/TGACCCATCC)CCAGC splice-acceptor-variant
rs886037960 Pathogenic 88,865(-) CTCAC(-/AC)CAGCC reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for NPRL3 Gene

Variant ID Type Subtype PubMed ID
dgv2689n100 CNV gain 25217958
dgv2690n100 CNV gain 25217958
esv1304431 CNV insertion 17803354
esv2422427 CNV duplication 17116639
esv2657149 CNV deletion 23128226
esv2760065 CNV gain 17122850
esv2760406 CNV gain+loss 21179565
esv32706 CNV loss 17666407
esv3552956 CNV deletion 23714750
esv3637536 CNV loss 21293372
esv3637537 CNV gain 21293372
esv3637539 CNV loss 21293372
esv3637540 CNV gain 21293372
nsv1037664 CNV gain 25217958
nsv1044142 CNV gain 25217958
nsv1045829 CNV gain 25217958
nsv1050893 CNV gain 25217958
nsv1070306 CNV deletion 25765185
nsv1129572 CNV tandem duplication 24896259
nsv1132870 CNV insertion 24896259
nsv1697 CNV insertion 18451855
nsv518291 CNV loss 19592680
nsv570924 CNV loss 21841781
nsv9317 CNV gain 18304495
nsv958218 CNV deletion 24416366

Variation tolerance for NPRL3 Gene

Gene Damage Index Score: 2.86; 48.28% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NPRL3 Gene

Human Gene Mutation Database (HGMD)
NPRL3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NPRL3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NPRL3 Gene

Disorders for NPRL3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for NPRL3 Gene - From: Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
epilepsy, familial focal, with variable foci
  • familial focal epilepsy with variable foci
secondary hypertrophic osteoarthropathy
  • bamberger-marie disease
myoblastoma
  • benign granular cell tumor
spherocytosis, type 3
  • hereditary spherocytosis type 3
focal epilepsy
  • localisation-related epilepsy
- elite association - COSMIC cancer census association via MalaCards
Search NPRL3 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NPRL3_HUMAN
  • Epilepsy, familial focal, with variable foci 3 (FFEVF3) [MIM:617118]: An autosomal dominant form of epilepsy characterized by focal seizures arising from different cortical regions, including the temporal, frontal, parietal, and occipital lobes. Seizure types commonly include temporal lobe epilepsy, frontal lobe epilepsy, and nocturnal frontal lobe epilepsy. Some patients may have intellectual disability or autism spectrum disorders. Seizure onset usually occurs in the first or second decades, although later onset has been reported, and there is phenotypic variability within families. A subset of patients have structural brain abnormalities. Penetrance of the disorder is incomplete. {ECO:0000269 PubMed:26285051, ECO:0000269 PubMed:26505888, ECO:0000269 PubMed:27173016}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Inactivating mutations and truncating deletions in the genes encoding GATOR1 proteins are detected in glioblastoma and ovarian tumors and are associated with loss of heterozygosity events. Inactivation of GATOR1 proteins promotes constitutive localization of mTORC1 to the lysosomal membrane and blocks mTORC1 inactivation following amino acid withdrawal (PubMed:23723238). {ECO:0000269 PubMed:23723238}.

Relevant External Links for NPRL3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NPRL3
genes like me logo Genes that share disorders with NPRL3: view

No data available for Genatlas for NPRL3 Gene

Publications for NPRL3 Gene

  1. Conservation of position and sequence of a novel, widely expressed gene containing the major human alpha-globin regulatory element. (PMID: 8575760) Vyas P. … Higgs D. (Genomics 1995) 2 3 4 64
  2. Familial cortical dysplasia caused by mutation in the mammalian target of rapamycin regulator NPRL3. (PMID: 26285051) Sim J.C. … Leventer R.J. (Ann. Neurol. 2016) 3 4 64
  3. Mutations in the mTOR pathway regulators NPRL2 and NPRL3 cause focal epilepsy. (PMID: 26505888) Ricos M.G. … Dibbens L.M. (Ann. Neurol. 2015) 3 4 64
  4. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. (PMID: 23723238) Bar-Peled L. … Sabatini D.M. (Science 2013) 3 4 64
  5. A genome-wide screen for regulators of TORC1 in response to amino acid starvation reveals a conserved Npr2/3 complex. (PMID: 19521502) Neklesa T.K. … Davis R.W. (PLoS Genet. 2009) 3 4 64

Products for NPRL3 Gene

  • Addgene plasmids for NPRL3

Sources for NPRL3 Gene

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